I think there's a distinction between prototypes of parts of the game and the full game.
I remember Carmack building a prototype of the texturing system for Rage to see if it would all work, so maybe the prototyping was always just an implicit part of JC's programming.
I think the distinction lies in always building production ready code.
You can build things to try out and experiment different modes of play or modes of rendering but the code you write should always be production ready. No taking shortcuts because "it's just a prototype".
I remember Carmack building a prototype of the texturing system for Rage to see if it would all work, so maybe the prototyping was always just an implicit part of JC's programming.